| Previous changeset 9:b3d513c7093e (2024-06-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997 |
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modified:
count-median.xml macros.xml |
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| diff -r b3d513c7093e -r 570505540a7b count-median.xml --- a/count-median.xml Mon Jun 17 11:47:05 2024 +0000 +++ b/count-median.xml Thu Oct 03 13:47:04 2024 +0000 |
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| @@ -1,10 +1,10 @@ <tool id="khmer_count_median" name="khmer: Count Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Count the median/avg k-mer abundance for each sequence</description> - <expand macro="bio_tools"/> <macros> <token name="@BINARY@">count-median.py</token> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version" /> @@ -21,7 +21,7 @@ <expand macro="input_countgraph_filename" /> </inputs> <outputs> - <data name="output_summary_filename" format="txt" + <data name="output_summary_filename" format="csv" label="${tool.name} on ${on_string}" /> </outputs> <tests> @@ -40,8 +40,8 @@ Count the median/avg k-mer abundance for each sequence in the input file, based on the k-mer counts in the given k-mer countgraph. Can be used to estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The -output file contains sequence id, median, average, stddev, and seq length; -fields are separated by spaces. For khmer 1.x count-median.py will split +output file contains sequence id, median, average, stddev, and seq length. +For khmer 1.x count-median.py will split sequence names at the first space which means that some sequence formats (e.g. paired FASTQ in Casava 1.8 format) will yield uninformative names. Use `--csv` to fix this behavior. |
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| diff -r b3d513c7093e -r 570505540a7b macros.xml --- a/macros.xml Mon Jun 17 11:47:05 2024 +0000 +++ b/macros.xml Thu Oct 03 13:47:04 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.0.0a3</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.01</token> <xml name="bio_tools"> <xrefs> @@ -34,7 +34,7 @@ #end if ]]> </token> - <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> + <token name="@THREADS@">--threads "\${GALAXY_SLOTS:-4}"</token> <xml name="tableinputs"> <conditional name="parameters"> <param name="type" type="select" label="Advanced Parameters" @@ -43,7 +43,7 @@ <option value="specific">Show</option> </param> <when value="simple"> - <param argument="" name="tablesize" type="select" label="Sample Type" display="radio"> + <param argument="--max-tablesize" name="tablesize" type="select" label="Sample Type" display="radio"> <option value="1e9" selected="true">Microbial Genome</option> <option value="2e9">Animal Transcriptome</option> <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option> @@ -51,8 +51,8 @@ </param> </when> <when value="specific"> - <param argument="--ksize" name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> - <param argument="--n_tables" name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> + <param argument="--ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" /> + <param argument="--n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" /> <param argument="--max-tablesize" name="tablesize_specific" type="text" value="1000000.0" label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" /> </when> @@ -90,11 +90,13 @@ help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." /> </xml> <xml name="abundance-histogram-output"> - <data name="output_histogram_filename" format="txt" - label="${tool.name} on ${on_string}: k-mer abundance histogram. The - columns are: (1) k-mer abundance, (2) k-mer count, (3) - cumulative count, (4) fraction of total distinct k-mers." /> + <data name="output_histogram_filename" format="csv" + label="${tool.name} on ${on_string}: k-mer abundance histogram" /> </xml> + <token name="@ABUNDANCE_HISTOGRAM_OUTPUT_HELP@"><![CDATA[ + The columns of the k-mer abundance histogram are: (1) k-mer abundance, (2) k-mer count, (3) cumulative count, (4) fraction of total distinct k-mers. +]]></token> + <xml name="output_sequences" token_extension=""> <collection name="sequences" type="list"> <discover_datasets pattern="(?P<name>.*)\.(?P<ext>fast[aq](\.gz)?)\.@EXTENSION@" directory="output" /> |